commit: ea635c5ba9ce7015a7f3cf0f1aa1b8341e9c0eab Author: Matthias Maier <tamiko <AT> gentoo <DOT> org> AuthorDate: Thu Dec 31 08:02:03 2015 +0000 Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> CommitDate: Thu Dec 31 08:02:21 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=ea635c5b
sci-mathematics/petsc: version bump to 2.6.3 Package-Manager: portage-2.2.26 sci-mathematics/petsc/ChangeLog | 5 + sci-mathematics/petsc/petsc-3.6.3.ebuild | 253 +++++++++++++++++++++++++++++++ 2 files changed, 258 insertions(+) diff --git a/sci-mathematics/petsc/ChangeLog b/sci-mathematics/petsc/ChangeLog index 861d62b..89fdf76 100644 --- a/sci-mathematics/petsc/ChangeLog +++ b/sci-mathematics/petsc/ChangeLog @@ -2,6 +2,11 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Id$ +*petsc-3.6.3 (31 Dec 2015) + + 31 Dec 2015; Matthias Maier <[email protected]> +petsc-3.6.3.ebuild: + sci-mathematics/petsc: version bump + 01 Sep 2015; Marius Brehler <[email protected]> petsc-3.5.3.ebuild, petsc-3.6.0.ebuild: sci-mathematics/petsc: Add subslot for fftw dependency diff --git a/sci-mathematics/petsc/petsc-3.6.3.ebuild b/sci-mathematics/petsc/petsc-3.6.3.ebuild new file mode 100644 index 0000000..dd3aed2 --- /dev/null +++ b/sci-mathematics/petsc/petsc-3.6.3.ebuild @@ -0,0 +1,253 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit eutils flag-o-matic fortran-2 python-any-r1 toolchain-funcs versionator + +MY_P="${PN}-$(replace_version_separator _ -)" + +DESCRIPTION="Portable, Extensible Toolkit for Scientific Computation" +HOMEPAGE="http://www.mcs.anl.gov/petsc/"; +SRC_URI="http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/${MY_P}.tar.gz"; + +LICENSE="petsc" +SLOT="0" +KEYWORDS="~x86 ~amd64" +IUSE="afterimage boost complex-scalars cxx debug doc fftw + fortran hdf5 hypre mpi mumps scotch sparse superlu threads X" +# Failed: imagemagick metis + +# hypre and superlu curretly exclude each other due to missing linking to hypre +# if both are enabled +REQUIRED_USE=" + afterimage? ( X ) + hdf5? ( mpi ) + hypre? ( cxx mpi ) + mumps? ( mpi scotch ) + scotch? ( mpi ) + ^^ ( hypre superlu ) +" +# imagemagick? ( X ) + +RDEPEND=" + virtual/blas + virtual/lapack + afterimage? ( media-libs/libafterimage ) + boost? ( dev-libs/boost ) + fftw? ( sci-libs/fftw:3.0[mpi?] ) + hdf5? ( sci-libs/hdf5[mpi?] ) + hypre? ( >=sci-libs/hypre-2.8.0b[mpi?] ) + mpi? ( virtual/mpi[cxx?,fortran?] ) + mumps? ( sci-libs/mumps[mpi?] sci-libs/scalapack ) + scotch? ( sci-libs/scotch[mpi?] ) + sparse? ( sci-libs/suitesparse >=sci-libs/cholmod-1.7.0 ) + superlu? ( sci-libs/superlu ) + X? ( x11-libs/libX11 ) +" +# metis? ( sci-libs/parmetis ) +# imagemagick? ( media-gfx/imagemagick ) + +DEPEND="${RDEPEND} + ${PYTHON_DEPS} + virtual/pkgconfig + dev-util/cmake +" +# cmake is used for parallel building +# in some configuration setups, legacy build is used (slow) + +# +# PETSc does not want its Makefiles to be invoked with anything higher than +# -j1. The underlying build system does automatically invoke a parallel +# build. This might not be what you want, but *hey* not your choice. +# +MAKEOPTS="${MAKEOPTS} -j1" + +S="${WORKDIR}/${MY_P}" + +src_prepare() { + epatch \ + "${FILESDIR}"/${PN}-3.6.0-disable-rpath.patch \ + "${FILESDIR}"/${PN}-3.6.0-fix_sandbox_violation.patch + + sed -i -e 's%/usr/bin/env python%/usr/bin/env python2%' configure || die +} + +src_configure() { + # bug 548498 + # PETSc runs mpi processes during configure that result in a sandbox + # violation by trying to open /proc/mtrr rw. This is not easy to + # mitigate because it happens in libpciaccess.so called by libhwloc.so, + # which is used by libmpi.so. + addpredict /proc/mtrr + + # petsc uses --with-blah=1 and --with-blah=0 to en/disable options + petsc_enable() { + use "$1" && echo "--with-${2:-$1}=1" || echo "--with-${2:-$1}=0" + } + # add external library: + # petsc_with use_flag libname libdir + # petsc_with use_flag libname include linking_libs + petsc_with() { + local myuse p=${2:-${1}} + if use ${1}; then + myuse="--with-${p}=1" + if [[ $# -ge 4 ]]; then + myuse="${myuse} --with-${p}-include=${EPREFIX}${3}" + shift 3 + myuse="${myuse} --with-${p}-lib=$@" + else + myuse="${myuse} --with-${p}-dir=${EPREFIX}${3:-/usr}" + fi + else + myuse="--with-${p}=0" + fi + echo ${myuse} + } + + # select between configure options depending on use flag + petsc_select() { + use "$1" && echo "--with-$2=$3" || echo "--with-$2=$4" + } + + local mylang + local myopt + + use cxx && mylang="cxx" || mylang="c" + use debug && myopt="debug" || myopt="opt" + + # environmental variables expected by petsc during build + export PETSC_DIR="${S}" + export PETSC_ARCH="linux-gnu-${mylang}-${myopt}" + + if use debug; then + strip-flags + filter-flags -O* + fi + + # C Support on Cxx builds is enabled if possible + # i.e. when not using complex scalars + # (no complex type for both available at the same time) + + # run petsc configure script + econf \ + scrollOutput=1 \ + CFLAGS="${CFLAGS}" \ + CXXFLAGS="${CXXFLAGS}" \ + LDFLAGS="${LDFLAGS}" \ + --with-shared-libraries \ + --with-single-library \ + --with-clanguage=${mylang} \ + $(use cxx && ! use complex-scalars && echo "with-c-support=1") \ + --with-petsc-arch=${PETSC_ARCH} \ + --with-precision=double \ + --with-gnu-compilers \ + --with-blas-lapack-lib="$($(tc-getPKG_CONFIG) --libs lapack)" \ + $(petsc_enable debug debugging) \ + $(petsc_enable mpi) \ + $(petsc_select mpi cc mpicc $(tc-getCC)) \ + $(petsc_select mpi cxx mpicxx $(tc-getCXX)) \ + $(petsc_enable fortran) \ + $(use fortran && echo "$(petsc_select mpi fc mpif77 $(tc-getF77))") \ + $(petsc_enable mpi mpi-compilers) \ + $(petsc_select complex-scalars scalar-type complex real) \ + --with-windows-graphics=0 \ + --with-matlab=0 \ + --with-cmake=cmake \ + $(petsc_enable threads pthread) \ + $(petsc_with afterimage afterimage \ + /usr/include/libAfterImage -lAfterImage) \ + $(petsc_with hdf5) \ + $(petsc_with hypre hypre \ + /usr/include/hypre -lHYPRE) \ + $(petsc_with sparse suitesparse) \ + $(petsc_with superlu superlu \ + /usr/include/superlu -lsuperlu) \ + $(petsc_with X x) \ + $(petsc_with X x11) \ + $(petsc_with scotch ptscotch \ + /usr/include/scotch \ + [-lptesmumps,-lptscotch,-lptscotcherr,-lscotch,-lscotcherr]) \ + $(petsc_with mumps scalapack \ + /usr/include/scalapack -lscalapack) \ + $(petsc_with mumps mumps \ + /usr/include \ + [-lcmumps,-ldmumps,-lsmumps,-lzmumps,-lmumps_common,-lpord]) \ + --with-imagemagick=0 \ + --with-python=0 \ + $(petsc_with boost) \ + $(petsc_with fftw) + +# not yet tested: +# python bindings, netcdf, fftw + +# failed dependencies, perhaps fixed in upstream soon: +# $(petsc_with metis parmetis) \ # needs metis too (>=5.0.2) +# $(petsc_with imagemagick imagemagick \ +# /usr/include/ImageMagick $($(tc-getPKG_CONFIG) --libs MagickCore)) \ +# $(petsc_enable threads pthreadclasses) \ +} + +src_install() { + # petsc install structure is very different from + # installing headers to /usr/include/petsc and lib to /usr/lib + # it also installs many unneeded executables and scripts + # so manual install is easier than cleanup after "emake install" + insinto /usr/include/${PN} + doins include/*.h* + insinto /usr/include/${PN}/${PETSC_ARCH}/include + doins ${PETSC_ARCH}/include/* + if use fortran; then + insinto /usr/include/${PN}/finclude + doins -r include/${PN}/finclude/* + fi + if ! use mpi ; then + insinto /usr/include/${PN}/mpiuni + doins include/mpiuni/*.h + fi + insinto /usr/include/${PN}/conf + doins lib/${PN}/conf/{variables,rules,test} + insinto /usr/include/${PN}/${PETSC_ARCH}/conf + doins ${PETSC_ARCH}/lib/${PN}/conf/{petscrules,petscvariables,RDict.db} + insinto /usr/include/${PN}/private + doins include/${PN}/private/*.h + + # fix configuration files: replace "${S}" by installed location + sed -i \ + -e "s:"${S}"::g" \ + "${ED}"/usr/include/${PN}/${PETSC_ARCH}/include/petscconf.h \ + "${ED}"/usr/include/${PN}/${PETSC_ARCH}/conf/petscvariables || die + sed -i \ + -e "s:-I/include:-I${EPREFIX}/usr/include/${PN}:g" \ + -e "s:-I/linux-gnu-cxx-opt/include:-I${EPREFIX}/usr/include/${PN}/${PETSC_ARCH}/include/:g" \ + "${ED}"/usr/include/${PN}/${PETSC_ARCH}/conf/petscvariables || die + sed -i \ + -e "s:usr/lib:usr/$(get_libdir):g" \ + "${ED}"/usr/include/${PN}/${PETSC_ARCH}/include/petscconf.h || die + + # add information about installation directory and + # PETSC_ARCH to environmental variables + cat >> 99petsc <<- EOF + PETSC_ARCH=${PETSC_ARCH} + PETSC_DIR=${EPREFIX}/usr/include/${PN} + EOF + doenvd 99petsc + + dolib.so ${PETSC_ARCH}/lib/*.so + dolib.so ${PETSC_ARCH}/lib/*.so.* + + if use doc ; then + einfo "installing documentation (this could take a while)" + dodoc docs/manual.pdf + dohtml -r docs/*.html docs/changes docs/manualpages + fi +} + +pkg_postinst() { + elog "The petsc ebuild is still under development." + elog "Help us improve the ebuild in:" + elog "http://bugs.gentoo.org/show_bug.cgi?id=53386"; +}
